I've been wanting to try out some web-based annotation tools for use in peer-review and collaboration, so I've installed a copy of Geof Glass' very cool Marginalia and imported an example document into it (with the author's permission) - feel free to add and edit annnotations (though please don't delete other people's annotations that might be useful). There's also a test page that doesn't store annotations, with some instructions.
Marginalia is really well made: it's all Javascript and PHP, with MySQL storage and all the communication done using Atom (which means you get an Atom feed of recent annotations for free).
It's very basic at the moment as there's no user control, so anyone can deface the annotations. What I'd like to see eventually is a wiki-like editing interface for the main content (with the ability to fork off new versions) and non-anonymous annotations, as well as voting by reviewers (+1, -1, abstain) on whether to accept an article for publication.
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I've not used it, but see this DocBook + SVN based option:
http://goshaky.com/goshaky/review-system/
Now that's cool. As you point out, it needs controls (so one cannot, as I did, stupidly delete others' annotations -- I made a note where I did it, sorry about that). I'd also prefer that annotators have to sign in. It also occurs to me that either I missed it or there's no way for multiple annotators to comment on the same section of text -- which will be necessary, as will some mechanism for commenting on others' annotations (e.g. the author could reply to criticism). There's an issue with running out of room; perhaps if the annotations were popups rather than off to the side?
Anyway, this is great. I wonder if Biology Direct would be interested in using it?
Actually, there is some accommodation for different users. Each annotation is stored with the id of the current user. In the Moodle version, there's a drop-down menu allowing you view another user's annotations (read-only). There is, however, no facility for viewing the annotations of multiple users at the same time; the Moodle version provides a summary page (with search and filter criteria) for this purpose.
The reason you're not seeing any of this here is that Marginalia isn't really a stand-alone application (it's intended to be integrated into another app), so the demo doesn't provide any log-in facilities. It's hard-coded to show and edit annotations by an anonymous user (this is explained in some mildly-outdated comments at the top of the HTML source).